Bowtie2 site-specific tweaks for fastq_screen with Bowtie2

* Unfortunately it uses UPPMAX-specific path to refer to the bowtie2 index. There is no Galaxy rsync indexes for those organisms, yet.

* Correct with statement for backwards compat with python 2.6.6.

* Cleanup and re-running benchmarks with @guillermo-carrasco fixes for memory_profiling and simNGS read trimming.